CoCoCoNet: conserved and comparative co-expression across a diverse set of species

Lee, J., Shah, M., Ballouz, S., Crow, M., Gillis, J. (May 2020) CoCoCoNet: conserved and comparative co-expression across a diverse set of species. Nucleic Acids Research. ISSN 0305-1048

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DOI: 10.1093/nar/gkaa348


Co-expression analysis has provided insight into gene function in organisms from Arabidopsis to zebrafish. Comparison across species has the potential to enrich these results, for example by prioritizing among candidate human disease genes based on their network properties or by finding alternative model systems where their co-expression is conserved. Here, we present CoCoCoNet as a tool for identifying conserved gene modules and comparing co-expression networks. CoCoCoNet is a resource for both data and methods, providing gold standard networks and sophisticated tools for on-the-fly comparative analyses across 14 species. We show how CoCoCoNet can be used in two use cases. In the first, we demonstrate deep conservation of a nucleolus gene module across very divergent organisms, and in the second, we show how the heterogeneity of autism mechanisms in humans can be broken down by functional groups and translated to model organisms. CoCoCoNet is free to use and available to all at, with data and R scripts available at

Item Type: Paper
CSHL Authors:
Communities: CSHL labs > Gillis Lab
CSHL Cancer Center Program > Gene Regulation and Inheritance Program
Depositing User: Adrian Gomez
Date: 11 May 2020
Date Deposited: 18 May 2020 15:44
Last Modified: 29 Oct 2020 19:02
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